GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iorA in Desulfovibrio vulgaris Hildenborough

Align Indolepyruvate oxidoreductase subunit IorA; IOR; Indolepyruvate ferredoxin oxidoreductase subunit alpha; EC 1.2.7.8 (characterized)
to candidate 207421 DVU1951 indolepyruvate ferredoxin oxidoreductase, alpha subunit, putative

Query= SwissProt::P80910
         (618 letters)



>lcl|MicrobesOnline__882:207421 DVU1951 indolepyruvate ferredoxin
           oxidoreductase, alpha subunit, putative
          Length = 616

 Score =  476 bits (1224), Expect = e-138
 Identities = 270/605 (44%), Positives = 365/605 (60%), Gaps = 20/605 (3%)

Query: 12  GDRLFLLGNEAAVRAAIESGVGVASTYPGTPSSEIGNVLSKIAKRAGIYFEFSINEKVAL 71
           G+R  LLGNEA VR A+E+G+ V + YPGTPSSE+ +   +I        E+S+NEKVAL
Sbjct: 11  GERHLLLGNEAIVRGALEAGINVVTCYPGTPSSEVPDTFRRIGGDGRYRLEYSVNEKVAL 70

Query: 72  EVAAAAAASGVRSFTFMKHVGLNVASDSFMSVAYTGVRAGMVVLSADDPSMFSSQNEQDN 131
           EV A AA +G  +   MKHVG+NVA+D  +++ YTG+  G+V+LSADDP   SSQNEQDN
Sbjct: 71  EVGAGAALAGALTLVTMKHVGVNVAADPLLTMTYTGLPGGLVLLSADDPGCHSSQNEQDN 130

Query: 132 RHYARLAWVPLLEPSNPQEILEYMNHAFELSEEYRIPVLLRTTTRVSHMRGVVEAGERRA 191
           R YAR A +P  EP+  QE  +    A  LS E + PVLLRTTTRV+H+RG V  G    
Sbjct: 131 RTYARFAGMPCFEPATAQEAKDMAREALLLSRETQQPVLLRTTTRVNHLRGGVTYGALPE 190

Query: 192 EPVKGFFRKNPEQFVPVPATARVMRRELVEKMKKLKRVADTSELNRVLNEDSESDLGIIA 251
                 F +NP +FVPVPA AR       + + ++  +A  S  N V     E  +G+IA
Sbjct: 191 PAAVVPFERNPRRFVPVPAVARARHFAQADVLGRVAELASASPWNTV---HGEGRIGVIA 247

Query: 252 SGGAFNYVYDALQTLGLD--VPVLKLGFTYPFPAGLVAEFLSGLEGVLVVEEVDSVMEKE 309
           SG +  Y+ DAL   GL+  V VL+LGFT+P P  L+ +FLSG + VLV+EE++ ++E++
Sbjct: 248 SGISRAYLADALHERGLEGRVKVLELGFTWPLPERLLVDFLSGCDKVLVLEELEPLLERD 307

Query: 310 VLAVATSEGLDVGVHGKLDGTLPEIYEYSEDIVRRAISGLTGIKSHEKGIEAP-----EL 364
           V A+    GL V V GK  G L    EYS  IV  A+S   G         +P     EL
Sbjct: 308 VRALVQRLGLGVDVTGK-GGVLTVFGEYSTTIVGDALSAFLGETPAAPVQCSPDAASMEL 366

Query: 365 PERPPALCPGCPHRAMYYSVRRAASELGIEGEDLIFPTDIGCYTLGIEPPYSAADYLLSM 424
           P RPP LC GC HRA+YY+VR+      + G+D  + +DIGCYTLG+ PP S AD+L  M
Sbjct: 367 PMRPPNLCAGCSHRAVYYAVRK------VFGDDAYYSSDIGCYTLGLLPPLSMADFLFCM 420

Query: 425 GSSVGTACGFSAATSQRIVSFIGDSTFFHAGIPPLINAVHNRQRFVLVILDNRTTAMTGG 484
           GSS+ +  GF+AA+ + +V++IGDSTFFH+GI  L NA+ N+   ++VILDN TTAMTG 
Sbjct: 421 GSSISSGSGFAAASGRPVVAYIGDSTFFHSGITGLANALFNKHDVLVVILDNGTTAMTGH 480

Query: 485 QPHPGLPVDGMGEEAPAISIEDITRACGVEFVETVNPMNIRRSSETIRRALQHESVAVVI 544
           QP+PG+    +G+    + IE I R CGVE V TV+P N++ +   +    Q   V V+I
Sbjct: 481 QPNPGVDAAVLGDACLHLDIEAIVRGCGVEQVATVHPYNLKATMAALEDMKQRTGVRVII 540

Query: 545 SRYPCMLSEGAVRGRPVRVDEEKCDLCLE---CLNELACPAIVEEDGRVFIDPLYCRGCT 601
           ++ PC+L       +  R      +   E   CL ELACPA   +   + ID   C GC 
Sbjct: 541 AQEPCVLYARRTLKKAARQTAYVAEQGPEVEACLAELACPAFRRDGQDIAIDSEQCSGCM 600

Query: 602 ICLQI 606
           +CLQ+
Sbjct: 601 VCLQV 605


Lambda     K      H
   0.319    0.137    0.398 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 902
Number of extensions: 36
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 618
Length of database: 616
Length adjustment: 37
Effective length of query: 581
Effective length of database: 579
Effective search space:   336399
Effective search space used:   336399
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory